CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
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TLDR
A tool is provided that predicts the most likely targets of CRISPR RNAs and is used to discover targets in newly sequenced genomic or metagenomic data, and features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and IIICRISPR/Cas systems are discovered.Abstract:
The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems.read more
Citations
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NCBI prokaryotic genome annotation pipeline
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Inhibition of CRISPR-Cas9 with Bacteriophage Proteins
Benjamin J. Rauch,Melanie R. Silvis,Judd F. Hultquist,Judd F. Hultquist,Christopher S. Waters,Michael J. McGregor,Michael J. McGregor,Nevan J. Krogan,Nevan J. Krogan,Joseph Bondy-Denomy +9 more
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Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28
Aaron Smargon,David Benjamin Turitz Cox,Neena Pyzocha,Kaijie Zheng,Kaijie Zheng,Kaijie Zheng,Ian Slaymaker,Ian Slaymaker,Ian Slaymaker,Jonathan S. Gootenberg,Omar Abudayyeh,Patrick Essletzbichler,Patrick Essletzbichler,Patrick Essletzbichler,Sergey Shmakov,Sergey Shmakov,Kira S. Makarova,Eugene V. Koonin,Feng Zhang +18 more
TL;DR: It is established that two class 2 CRISPR-Cas systems that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, can achieve RNA interference when heterologously expressed.
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Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration
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Computational approaches to predict bacteriophage–host relationships
Robert Edwards,Katelyn McNair,Karoline Faust,Jeroen Raes,Jeroen Raes,Bas E. Dutilh,Bas E. Dutilh,Bas E. Dutilh +7 more
TL;DR: Analysis of 820 phages with annotated hosts shows how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications.
References
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